title: Transcriptional profilling of hESC with and without 17q gain upon induction of replicative stress through HU treatment [targeted exome sequencing]

city: Ghent

first: Kaat

last: Durinck

address: Corneel Heymanslaan 10

department: Biomolecular Medicine

country: Belgium

institute: Center for Medical Genetics

type: Genome variation profiling by high throughput sequencing

summary: Human embryonic stem cells (hESC) and cancer cells rapidly divide with a short G1/S-phase causing increased replicative stress (RS). Since both in vitro cultured hESCs and most high-risk neuroblastomas have large chromosome 17q gains (17q+), we hypothesize that this may provide a "RS-resistance phenotype". We co-cultured parental cells and a derived hESC line with 17q+ under normal growth conditions and under RS. We could show a proliferative ad-vantage of hESC with 13q+17q+ over wild type by measurement of the cumulative growth and molecular analysis for chromosomal copy number analysis. To monitor effects of 17q+ on RS-resistance, cell cycle and transcriptome analysis were performed. In conclusion, we show that extra chromosomal aberrations, such as 17q+, provide proliferative advantage to hESC under RS and suggest that this phenomenon explains the high incidence of 17q+ in in vitro cultured hESC lines.

overall_design: Samples were collected at each splitting moments of hESC with and without 17q gain, and of the 1:1 mixed culture; under normal growth conditions (PBS) or conditions of replicative stress (150 µM HU), for 2 biological replicates

first: Liselot

last: Mus

first: Stéphane

last: Van Haver

first: Mina

last: Popovic

first: Wim

last: Trypsteen

first: Steve

last: Lefever

first: Nadja

last: Zeltner

first: Yudelca

last: Ogando

first: Eva

last: Jacobs

first: Ellen

last: Sanders

first: Christophe

last: Van Neste

first: Suzanne

last: Vanhauwaert

first: Bieke

last: Decaesteker

first: Dieter

last: Deforce

first: Filip

last: van Nieuwerburgh

first: Pieter

last: Mestdagh

first: Jo

last: Vandesompele

first: Björn

last: Menten

first: Katleen

last: De Preter

last: Heindryckx

first: Lorenz

last: Studer

first: Stephen

last: Roberts

first: Frank

last: Speleman


title: Transcriptional profilling of hESC with and without 17q gain upon induction of replicative stress through HU treatment [sWGS]

status: Public on May 11 2021

first: Kaat

last: Durinck

first: Liselot

middle: M

last: Mus

first: Stéphane

last: Van Haver

first: Mina

last: Popovic

first: Wim

last: Trypsteen

first: Steve

last: Lefever

last: Zeltner


title: Transcriptional profilling of hESC with and without 17q gain upon induction of replicative stress through HU treatment [RNA-Seq]

type: Expression profiling by high throughput sequencing

overall_design: Samples were collected at 6 consecutive splitting moments of hESC with and without 17q gain, under normal growth conditions (PBS) or conditions of replicative stress (150 µM HU), for 2 biological replicates

first: Nadja

first: Yudelca

last: Ogando

first: Eva

last: Jacobs

first: Ellen

last: Sanders

first: Christophe

last: Van Neste

first: Suzanne

last: Vanhauwaert

last: Decaesteker

last: Deforce


title: Flightless I is a novel catabolic factor of chondrocytes that promotes hypertrophy and cartilage degeneration in osteoarthritis

status: Public on May 10 2021

city: Sapporo

first: Mohamad Alaa

last: Terkawi

state: Hokkaido

address: Kita-15, Nish-7, Kita-ku

department: Department of Orthopedic Surgery

country: Japan

institute: Hokkaido University

summary: Synovial macrophages that are activated by cartilage fragments initiate synovitis, a condition that promotes hypertrophic changes in chondrocytes leading to cartilage degeneration in OA. In this study, we analyzed the molecular response of chondrocytes under condition of this type of stimulation to identify a molecular therapeutic target. Stimulated macrophages promoted hypertrophic changes in chondrocytes resulting in production of matrix-degrading enzymes of cartilage. Among the top-upregulated genes, FliI was found to be released from activated chondrocytes and exerted autocrine/paracrine effects on chondrocytes leading to an increase in expression of catabolic and hypertrophic factors. Silencing FliI in stimulated cells significantly reduced expression of catabolic and hypertrophic factors in cocultured chondrocytes. Our further results demonstrated that the FliI-TLR4-ERK1/2 axis is involved in the hypertrophic signaling of chondrocytes and catabolism of cartilage. Our findings provide a new insight into the pathogenesis of OA and identify a potentially new molecular target for diagnostics and therapeutics.

overall_design: RNA-seq for chondrocytes stimulated by cartilage fragments activated macrophage.

first: Mohamad

middle: A

first: Taku

last: Ebata

first: Tomohiro

last: Onodera

first: Norimasa

last: Iwasaki


title: Coordinate regulation of ELF5 and EHF at the chr11p13 modifier region

city: Cleveland

first: Ann

last: Harris

state: OH

address: 10900 Euclid Ave

country: USA

institute: Case Western Reserve Uni

type: Genome binding/occupancy profiling by high throughput sequencing

summary: E74-like factor 5 (ELF5) and ETS-homologous factor (EHF) are epithelial selective ETS family transcription factors (TFs) encoded by genes at chr11p13, a region associated with cystic fibrosis (CF) lung disease severity. EHF controls many key processes in lung epithelial function so its regulatory mechanisms are important. Using CRISPR/Cas9 technology, we removed three cis-regulatory elements (CREs) from the chr11p13 region in airway epithelial cells. Deletion of two enhancers and one CRE within a stretch enhancer at the EHF locus caused subtle changes in chromatin architecture, and though EHF expression did not change, ELF5 abundance increased. ELF5 is normally very low in airway cells so we next examined cell types that express more ELF5 (LNCaP and T47D). ATAC-seq experiments in these lines revealed novel peaks of open chromatin (potential CREs) at the 5’ end of chr11p13 that were associated with an expressed ELF5 gene. Furthermore, 4C-seq assays identified direct interactions between the active ELF5 promoter and sites within the EHF locus, suggesting coordinate regulation between these TFs. ChIP-seq for ELF5 in T47D cells revealed ELF5 occupancy within EHF introns 1 and 6 and siRNA-mediated depletion of ELF5 repressed EHF expression. These results define a new role for ELF5 in lung epithelial biology.

overall_design: IDR OMNI-ATAC-seq profiles of open chromatin were generated from 2 independent replicates of libraries for 3 cell lines: Calu3, LNCaP, and T47D

first: Shiyi

last: Yin

first: Jenny

middle: L

last: Kerschner


title: Transcriptional profilling of hESC with and without 17q gain upon induction of replicative stress through HU treatment

first: Kaat

last: Durinck

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Foxp3 enhancers synergize to maximize regulatory T cell suppressive capacity [TCR-seq]

city: Memphis

first: Beisi

last: Xu

state: Tennessee

address: 262 Danny Thomas Pl

department: Center for Applied Bioinformatics

institute: St Jude Children's Research Hosipital

summary: Treg cells bearing a diverse antigen receptor repertoire suppress pathogenic T cells and maintain immune homeostasis during their long lifespan. How their robust function is determined genetically remains elusive. Here, we investigate the regulatory space of the cis-regulatory elements of Treg lineage–specifying factor Foxp3. Foxp3 enhancers are known as distinct readers for environmental cues in promoting Treg cell induction or lineage stability. However, their single deficiencies cause mild, if any, immune dysregulation, leaving the key transcriptional mechanisms determining Foxp3 expression and thereby Treg suppressive capacity uncertain. We examined the collective activities of Foxp3 enhancers and found that they coordinate to maximize Treg cell induction, Foxp3 expression level, or lineage stability through distinct modes and that ablation of synergistic enhancers led to lethal autoimmunity in young mice. Thus, the induction and maintenance of a diverse, stable Treg cell repertoire rely on combinatorial Foxp3 enhancers, suggesting broad, stage-specific, synergistic activities of cell-intrinsic factors and -extrinsic cues in determining Treg suppressive capacity.

overall_design: We examined the collective activities of Foxp3 enhancers and found CNS0 and CNS3 coordinate to maximize Treg cell induction. To characterize the impact of CNS0 and CNS3 single and double deficiencies on Treg cell TCR repertorie, we performed bulk TCR-sequencing of the total Treg cells isolated from the peripheral lymphoid organs of GFP, CNS0KO, CNS3KO, and CNS03DKO mice at 16-days of age. Treg cells sorted from spleen, skin draining lymph nodes, mesenteric lymph node were pooled for individual male mouse.

first: Xinying

last: Zong

first: Xiaolei

last: Hao

first: Yongqiang

last: Feng


title: Hspa8 and ICAM-1 identified as damage-induced mediators of gd T cell activation

city: La Jolla

first: Deborah

last: Witherden

state: CA

address: 10550 North Torrey Pines Rd

institute: Scripps Research

summary: Here we identify a novel members of a gamma delta T cell "wound signature" that are upregulated following wounding and mediate the gamma delta T cell wound response. RNA-seq analysis of wounded and non-wounded epidermis was initially used to identify two new wound signature proteins (ICAM1 and HSPA8)

overall_design: RNA-seq data was generated from mouse whole epidermis from non-wounded skin and 2-hours post-wounding

first: Margarete

middle: D

last: Johnson

first: Michel

middle: F

last: Otuki

first: Daniela

last: Cabrini

first: Ross

last: Rudolph

first: Wendy

last: Havran


title: Foxp3 enhancers synergize to maximize regulatory T cell suppressive capacity [Capture-C]

overall_design: Capture-C was used to assess the three-dimensional chromatin architecture around the Foxp3 locus in Treg precursor cells (i.e., CD4 naïve T cells), ASC-treated iTreg cells, and natural Treg cells.

first: Shaela

last: Wright

first: Chunliang

last: Li

first: Jun


title: RNA sequencing on iPSC-derived iSOX9-astrocytes

city: Leuven

first: Jonathan

last: De Smedt

address: ON4 - Herestraat 49 PB804

department: Development and Regeneration

institute: Stem Cell Institute Leuven

summary: We generated a stable healthy and diseased (with ALS-linked FUS-R521H mutation) iPSC line containing the coding sequence of SOX9 under a Tet-on promotor in the safe harbor AAVS1 locus via recombinase-mediated cassette exchange. This allows the induction of SOX9 expression after doxycycline addition and generates in this way PSC-derived astrocytes. RNASeq is performed on these healthy and diseased iSOX9-astrocytes at an early and late timepoint. In addition, we included commercially available PSC-derived astrocytes (called "iCell") and fetal human primary astrocytes (called "fHA").

overall_design: Expression characterisation of iSOX9-astrocytes: we included early and late iSOX9 astrocytes generated from healthy and diseased iPSCs. In addition, iCell and fHA cells were included. All samples were sequenced in triplicate (3 independent differentiation for the iSOX9-astrocytes).

first: Katrien

last: Neyrinck

first: Johanna

last: Van Den Daele

first: Tim

last: Vervliet

first: Keimpe

last: Wierda

first: Melissa

last: Nijs

first: Tom

last: Vanbokhoven

first: Astrid

last: D'hondt

first: Mélanie

last: Planque

first: Sarah

last: Fendt

first: Pei

middle: Y

last: Shih

first: Frederik

last: Seibt

first: Juan

last: Pita Almenar

first: Mohamed

last: Kreir

first: Devesh

last: Kumar

first: Vania

last: Broccoli

first: Geert

last: Bultynck

first: Andreas

last: Ebneth

first: Alfredo

last: Cabrera-Socorro

first: Catherine

last: Verfaillie


title: Foxp3 enhancers synergize to maximize regulatory T cell suppressive capacity [Cut&Run]

first: Beisi

last: Xu

overall_design: CUT&RUN sequencing was used to assess the histone modifications (H3K4me3 and H3K27ac) and RNA polymerase II (Pol II) distribution around the Foxp3 locus in regulatory T cells of wild-type and Foxp3 enhancer deficiencies.

first: Minghong

last: He

first: Xinying

last: Zong

first: Yongqiang

last: Feng


title: Foxp3 enhancers synergize to maximize regulatory T cell suppressive capacity [ATAC-Seq]

overall_design: ATAC sequencing was used to assess the chromatin architecture in regulatory T cells and naïve CD4 T cells of wild-type and Foxp3 enhancer deficiencies.

first: Jun

last: Li


title: Foxp3 enhancers synergize to maximize regulatory T cell suppressive capacity [Bisulfite-Seq]

type: Methylation profiling by high throughput sequencing

overall_design: Genome-wide bisulfite sequencing (40x coverage) was performed with regulatory T cells isolated from mixed bone marrow chimeric mice generated with bone marrows from male donors of CD45.1 wild-type mice and CD45.2 mice of indicated genotypes to reveal the effect of Foxp3 enhancer deficiencies on local DNA methylation status.

first: Yiping

last: Fan


title: A domesticated Harbinger transposase forms a complex with HDA6 and promotes histone H3 deacetylation at genes but not TEs in Arabidopsis

city: Shenzhen

first: Xishi

last: Zhou

address: No 7, Pengfei Road

country: China

institute: Shenzhen agricultural Genome Research Institute, Chinese Academy of Agricultural Sciences

summary: In eukaryotes, histone acetylation is a major modification on histone N-terminal tails that is tightly connected to transcriptional activation. HDA6 is a histone deacetylase involved in the transcriptional regulation of genes and transposable elements (TEs) in Arabidopsis thaliana. HDA6 has been shown to participate in several complexes in plants, including a conserved SIN3 complex. Here, we uncover a novel protein complex containing HDA6, several Harbinger transposon-derived proteins (HHP1, SANT1, SANT2, SANT3, and SANT4), and MBD domain-containing proteins (MBD1, MBD2, and MBD4). We show that mutations of all four SANT genes in the sant-null mutant cause increased expression of the flowering repressors FLC, MAF4, and MAF5, resulting in a late flowering phenotype. Transcriptome deep sequencing reveals that while the SANT proteins and HDA6 regulate the expression of largely overlapping sets of genes, TE silencing is unaffected in sant-null mutants. Our global histone H3 acetylation profiling shows that SANT proteins and HDA6 modulate gene expression through deacetylation. Collectively, our findings suggest that Harbinger transposon-derived SANT domain-containing proteins are required for histone deacetylation and flowering time control in plants.

overall_design: For RNA-seq: three independent biological replicates of wild-type(Col-0), hhp1, mbd 1/2/4, sant1234-null and hda6 were used for RNA deep sequencing assay. Total RNA was extracted from 12-day-old Arabidopsis seedlings growing on 1/2 MS medium plates with TRIzol reagent (Invitrogen). mRNA-seq libraries were built according to the manufacturer’s protocol (NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA)) and paired-end sequenced on an Illumina NovaSeq 6000 platform. For ChIP-seq: three biological replicates of 12-day-old wild-type(Col-0), sant1234-null and hda6 seedlings growing on 1/2 MS medium plates were used for histone H3 modification ChIP-seq experiment. Sequencing libraries were generated using NEBNext® Ultra™ DNA Library Prep Kit for Illumina® (NEB, USA) and then paired-end sequenced on Illumina NovaSeq 6000 platform. We used anti-acetylated Histone H3 antibody (Merck Millipore, 06-599). Each replicate contained two dataset: ChIP and input (to avoid background interference).

first: Cuijun

last: Zhang


title: Next Generation Sequencing Analysis of Mycfl/fl and MycΔIE, ERT2 intestinal transcriptomes

city: Bethesda

first: Yuhong

last: Luo

state: MD

address: 37 Convent Dr

department: NCI

institute: NATIONAL INSTITUTES OF HEALTH

summary: Non-alcoholic fatty liver disease (NAFLD) is the most common chronic liver disorder in developed countries, with extremely limited therapeutic options. MYC is a highly pleiotropic transcription factor with broad biological functions. However, the effect of intestinal MYC on metabolic diseases has not been studied. Here, an unexpected role for intestinal MYC in NAFLD was uncovered. MYC was increased in ileum biopsies from obese people and positively correlated with body-mass index. Intestine-specific reduction of MYC in mice improved high-fat diet (HFD) -induced obesity and hepatic steatosis. Mechanistically, reduced expression of MYC in the intestine promoted glucagon-like peptide-1 (GLP-1) production and secretion via upregulating carbohydrate-responsive element binding protein (ChREBP) and solute carrier family 2, member 2 (GLUT2)/solute carrier family 5, member 1 (SGLT1), respectively. Furthermore, 10058-F4, a MYC inhibitor, had therapeutic effects on HFD-induced metabolic disorders, accompanied by increased GLP-1 and reduced ceramides in the serum. This study highlights intestinal MYC as a putative drug target against NAFLD.

overall_design: Bulk RNA-seq of RNA isolated from the intestine of HFD-fed Mycfl/fl and MycΔIE, ERT2 mice.

first: Frank

middle: J

last: Gonzalez


title: The SWI/SNF chromatin remodeling complex helps resolve R-loop-mediated transcription-replication conflicts

city: Seville

first: Andrés

last: Aguilera

address: Av. Américo Vespucio 24

department: Genome BIology

country: Spain

institute: CABIMER, Universidad de Sevilla

summary: ATP-dependent chromatin remodelers are commonly mutated in human cancer. Mammalian SWI/SNF complexes comprise three conserved multi-subunit chromatin remodelers (cBAF, ncBAF and PBAF) that share the BRG1 (also known as SMARCA4) subunit responsible for the main ATPase activity. BRG1 is the most frequently mutated Snf2-like ATPase in cancer. Here we have investigated the role of SWI/SNF in genome instability, a hallmark of cancer cells, given its role in transcription, DNA replication and DNA damage repair. We show that depletion of BRG1 increases R-loops and R-loop-dependent DNA breaks, as well as transcription-replication conflicts. BRG1 colocalizes with R-loops and replication fork blocks, as determined by FANCD2 foci, with BRG1 depletion being epistatic to FANCD2 silencing. Our study, extended to other components of SWI/SNF, uncovers a key role of the SWI/SNF complex, in particular cBAF, in helping resolve R-loop-mediated transcription-replication conflicts; thus, unveiling a novel mechanism by which chromatin remodeling protects genome integrity.

overall_design: Examination of genome-wide RNA-DNA hybrids accumulation in control (siC) and BRG1-depleted (siBRG1) K562 cells.

first: Aleix

last: Bayona-Feliu

first: Sonia

last: Barroso

first: Sergio

last: Muñoz


title: Next Generation Sequencing of Acidosis Response in Intestinal Epithelial Cells

city: Aurora

first: Ian

last: Cartwright

state: Colorado

department: Medicine

institute: University of Colorado Anschutz Medical Campus

summary: Purpose: The goal of this study is to define the impact of extracellular acidosis on transcriptional regulation in intestinal epithelial cells. We identify a significant induction of CREB target genes and upregulation of several genes associated with MAPK signaling. This work provides a frame work for the identification of acidosis signaling pathway in intestinal epithelial cells

overall_design: mRNA profiles of T84, human intestinal epithelial cells, treated wth pH 7.4 or 6.0 Hanks buffered saline for 3 or 6hr

first: Sean

middle: P

last: Colgan


title: A p53-dependent translational program directs tissue-selective phenotypes in a model of ribosomopathies

status: Public on May 09 2021

city: Stanford

first: Gerald

last: Tiu

state: California

address: 279 Campus Dr., Beckman Center B309

institute: Stanford University

summary: In ribosomopathies, perturbed expression of ribosome components leads to tissue-specific phenotypes. What accounts for such tissue-selective manifestations as a result of mutations in the ribosome, a ubiquitous cellular machine, has remained a mystery. Combining mouse genetics and in vivo ribosome profiling, we observe limb patterning phenotypes in ribosomal protein (RP) haploinsufficient embryos and uncover selective translational changes of transcripts controlling limb development. Surprisingly, both loss of p53, which is activated by RP haploinsufficiency, and augmented protein synthesis rescue these phenotypes. These findings are explained by the identification that p53 functions as a master regulator of protein synthesis, at least in part, through transcriptional activation of 4E-BP1. 4E-BP1, a key translational regulator, in turn, facilitates selective changes in the translatome downstream of p53, and thereby explains how RP haploinsufficiency may elicit specificity to gene expression. These results provide an integrative model to understand how in vivo tissue-specific phenotypes emerge in ribosomopathies.

overall_design: Ribosome profiling from E10.5 mouse forelimbs (N=3 of each genotype): Rps6lox/+;Trp53+/+, Prx1Cre;Rps6lox/+;Trp53+/+, Rps6lox/+;Trp53-/-, Prx1Cre;Rps6lox/+;Trp53-/-

middle: C

first: Craig

middle: H

last: Kerr

last: Forester

first: Pallavi

middle: S

last: Krishnarao

first: Hannah

last: Rosenblatt

first: Nitin

last: Raj

first: Travis

last: Lantz

first: Olena

last: Zhulyn

first: Margot

middle: E

last: Bowen

first: Leila

last: Shokat

first: Laura

last: Attardi

first: Davide

last: Ruggero

first: Maria

last: Barna


title: Tcf21+ mesenchymal cells contribute to testis somatic cell development, homeostasis, and regeneration

status: Public on May 08 2021

city: Ann Arbor

first: Qianyi

last: Ma

state: MI

address: 1141 E Catherine St

department: Human Genetics

institute: University of Michigan

summary: Testicular development and function relies on interactions between somatic cells and the germline, but similar to other organs, regenerative capacity decline in aging and disease. Whether the adult testis maintains a reserve progenitor population with repair or regenerative capacity remains uncertain. Here, we characterized a recently identified mouse testis interstitial population expressing the transcription factor Tcf21. We found that Tcf21+ cells are bipotential somatic progenitors present in fetal testis and ovary, maintain adult testis homeostasis during aging, and act as reserve somatic progenitors following injury. In vitro, Tcf21+ cells are multipotent mesenchymal progenitors which form multiple somatic lineages including Leydig and myoid cells. Additionally, Tcf21+ cells resemble resident fibroblast populations reported in other organs having roles in tissue homeostasis, fibrosis, and regeneration. Our findings reveal that the testis, like other organs, maintains multipotent mesenchymal progenitors that can be leveraged in development of future therapies for hypoandrogenism and/or infertility.

overall_design: Drop-seq of in-vitro differentiated Leydig cells

first: Saher

last: Hammoud


title: Epigenomic Regulation of Human T-Cell Leukemia Virus by Chromatin-Insulator CTCF

city: St. Louis

first: Jacqueline

last: Payton

state: MO

address: 660 S. Euclid Ave

department: Pathology and Immunology

institute: Washington University School of Medicine

summary: We compared histone modifications of wild type and HTLV-1ΔCTCF provirus  by ChIP sequencing and observed that loss of the vrial CTCF binding site in HTLV-1 results in increased histone methylation 5’ and 3’ of the CTCF site, suggesting that CTCF binding may act as a boundary element to epigenetic modification.

sample_organism:
Homo sapiens
Human T-cell leukemia virus type I

overall_design: Examine H3K4me3, H3K36me3 and H3K27me3 marks associated with the wild type and mutant HTLV-1 provirus in PBMCs and JET cells

first: Xiaogang

last: Cheng

first: Ancy

last: Joseph

first: Lee

last: Ratner


title: RNASEQ based transcriptome profiling of cold  responsive genes in  Fragaria vesca genotypes with differing sensitivity to cold

city: Oslo

first: Relindis

middle: Ghai

last: Njah

address: Blindernveien 31

department: Department of Biosciences

country: Norway

institute: University of Oslo

summary: By using high through put Illumina based  sequencing approach, we generated RNASEQ data for leaves and crowns of Alta and NCGR1363 at 0H and 42D exposure to temperature stress. We present the expression profile of 896 putative candidate genes identified within a QTL  associated with freezing tolerance. Expression profiles  revealed genotype specific cold responsive expression patterns in one group of candidates and expression differences between genotypes prior to treatment for many of the genes.

overall_design: Evaluation of transcript expression profiles in cold treated  crown and leaf tissues of Alta and NCGR1363 relative to controls

first: Robert

last: Wilson

first: Paul

last: Grini

middle: G


title: Foxp3 enhancers synergize to maximize regulatory T cell suppressive capacity

first: Beisi

last: Xu


title: Identification of Genes and miRNAs Affecting Pre-harvest Sprouting in Rice (Oryza sativa L.) by Transcriptome and Small RNAome Analyses

status: Public on May 07 2021

city: SEOUL

first: Chanseok

last: Shin

address: Gwanak-gu Daehak-dong

country: South Korea

institute: Seoul National University

summary:
Purpose: The goal of our study is to compare two different ecotypes of Oryza sativa L., PHS-susceptible rice trait and PHS-resistant rice trait under three different maturation stages and two different tissues, embryo and endosperm of rice seeds with profile of RNA-seq.
Methods: Oryza sativa. L mRNA profiles of two different ecotypes with 3 different maturation stages and 2 different tissues were generated by NGS, in duplicate, following Illumina NGS workflow. qRT–PCR validation was performed using SYBR Green assays.
Results: We found the differentially expressed genes (DEGs) between PHS-susceptible rice trait and PHS-resistant rice trait according to the three different seed maturation stages. In DEGs, gene ontology (GO) analysis and Mapman analysis were performed, and we discovered genes related to plant hormones and heat stress, which are not yet reported. These genes were validated through qRT-PCR, and it is likely to be highly related to seed dormancy.
Conclusions: Our study represents the analysis of rice seed transcriptomes under two different ecotypes, three different seed maturation stages and two different tissues (Embryo and endosperm). Our results show that seed dormancy is affected and regulated by a plant hormones and heat stress. This study might provide a foundation for understanding dynamics of seed dormancy during the seed development and overcoming pre-harvest sprouting.

overall_design: mRNA profiles of two different ecotypes of rice (Oryza sativa L.)

first: Minsu

last: Park

first: Woochang

last: Choi

first: Sang-Yoon

first: Hongman

last: Moon

first: Dowhan

last: Lee

first: Yun-Shil

last: Gho

first: Ki-Hong

last: Jung

first: Jong-Seong

last: Jeon


title: RNA sequencing analysis of CD11b+ peritoneal macrophages from WT (C57BL/6), Lum-/- and Bgn-/- mouse.

city: New York

first: Shukti

last: Chakravarti

state: New York

address: 430 E 29th St

department: Department of Ophthalmology and Pathology

institute: NYU Langone Medical Center

summary: Purpose: To compare transcriptomic changes between untreated and LPS or CpG treated groups in WT, Lum-/- and Bgn-/- peritoneal macrophages.

overall_design: CD11b+ cells isolated from WT/Lum-/-/Bgn-/- mice peritoneal lavage using CD11b+ selection kit (Stemcell Technology). Cells were treated with either LPS/CpG only or pretreated with recombinant lumican/biglycan followed by LPS/CpG treatment.

first: George

last: Maiti

first: Jihane

last: Frikeche

first: Asim

last: Biswas

first: Carly

last: Lam

first: Vishal

last: Shinde

first: Marie

last: Samanovic

first: Jonathan

last: Kagan

first: Mark

last: Mulligan


title: Molecular bases of P450-mediated resistance to the neonicotinoid insecticide imidacloprid in the mosquito Ae. aegypti

city: Saint Martin d'Hères

first: Stéphane

last: REYNAUD

address: 2233 rue de la piscine

country: France

institute: Grenoble-Alpes University

summary: Resistance to chemical insecticides including pyrethroids, the main insecticide class used against mosquitoes, led to a regain of interest for neonicotinoids. In this context, the present study aims at characterizing the molecular basis of neonicotinoid resistance in the mosquito Aedes aegypti. Resistance mechanisms were studied by combining transcriptomic and genomic data obtained from a laboratory strain selected at the larval stage for 30 generations with imidacloprid (Imida-R line). After thirty generations of selection, larvae of Imida-R line showed a 8-fold increased resistance to imidacloprid and a significant cross-tolerance to the pyrethroids permethrin and deltamethrin. Cross-resistance to pyrethroids was only observed in adults when larvae were previously exposed to imidacloprid suggesting a low but inducible expression of resistance alleles at the adult stage. Resistance of the Imida-R line was associated with a slower larval development time in females. Multiple detoxification enzymes were over-transcribed in larvae in association with resistance including the P450s CYP6BB2, CYP9M9 and CYP6M11 previously associated with pyrethroid resistance. Some of them together with their redox partner NADPH P450 reductase were also affected by non-synonymous mutations associated with resistance. Combining genomic and transcriptomic data allowed identifying promoter variations associated with the up-regulation of CYP6BB2 in the resistant line. Overall, these data confirm the key role of P450s in neonicotinoid resistance in Ae. aegypti and their potential to confer cross-resistance to pyrethroids, raising concerns about the use of neonicotinoids for resistance management in this mosquito species.

overall_design: mRNAseq  from Aedes aegypti  4th stage Larvae

first: S

last: Reynaud


title: Notch-Induced Endoplasmic Reticulum-Associated Degradation Governs Thymocyte β Selection

city: Houston

first: Fanglue

last: Peng

state: TX

address: One Baylor Plaza

department: Molecular and Cellular Biology

institute: Baylor College of Medicine

summary: β -selection imposes a considerable demand for new protein synthesis of the newly rearranged Tcrβ gene and the multiple factors that execute the transcriptional and metabolic programs demanded by DN thymocyte proliferation. However, how proteome homeostasis or “proteostasis” is regulated during thymocyte development is largely unknown. Here, we show that the endoplasmic reticulum (ER)- associated degradation (ERAD), but not the unfolded protein response (UPR), is the master regulator of physiological ER proteostasis in immature DN thymocytes. The ERAD machinery was critically required for successful β-selection of DN3 thymocytes and consequently, ERAD deficiency impeded αβ T cell development. The Sel1L-Hrd1 complex is the most conserved branch of mammalian ERAD machinery. Deletion of Sel1l impaired DN3 to DN4 thymocyte transition and severely impaired αβ T cell development. Mechanistically, Sel1l deficiency induced unresolved ER stress that triggered thymocyte apoptosis through the PERK pathway. This study revealed the stringent protein quality control through the SEL1L-ERAD pathway is required for successful b-selection and the development of the ab T cells that mediate adaptive immunity.

overall_design: DN3 mRNA profiles of 6-week-old wild type (WT) and Sel1l-f/f hCD2cre+ conditional knockout mice

first: Xi

last: Chen

first: Xia

last: Liu

first: Jingjing

last: Yu


title: The deacylase SIRT5 supports melanoma viability by regulating chromatin dynamics.

first: David

middle: B

last: Lombard

state: Michigan

address: 3015 BSRB, 109 Zina Pitcher Place

department: Pathology

institute: University of Michigan Ann Arbor

summary: Cutaneous melanoma remains the most lethal skin cancer, and ranks third among all malignancies in terms of years of life lost. Despite the advent of immune checkpoint and targeted therapies, only roughly half of patients with advanced melanoma achieve a durable remission. SIRT5 is a member of the sirtuin family of protein deacylases that regulate metabolism and other biological processes. Germline Sirt5 deficiency is associated with mild phenotypes in mice. Here we show that SIRT5 is required for proliferation and survival across all cutaneous melanoma genotypes tested, as well as uveal melanoma, a genetically distinct melanoma subtype that arises in the eye, and is incurable once metastatic. Likewise, SIRT5 is required for efficient tumor formation by melanoma xenografts, and in an autochthonous mouse Braf;Pten-driven melanoma model. Via metabolite and transcriptomic analyses, we find that SIRT5 is required to maintain histone acetylation and methylation levels in melanoma cells, thereby promoting proper gene expression. SIRT5-dependent genes notably include MITF, a key lineage-specific survival oncogene in melanoma, and the c-MYC proto-oncogene. SIRT5 may represent a novel, druggable genotype-independent addiction in melanoma.

overall_design:
RNA-seq was performed on A2058, A375, and SKMEL-2 cell lines infected with either control or SIRT5 shRNA (KD1 or KD2), for a total of 27 samples on the Illumina HiSeq4000 with 50nt paired-end sequencing. Alignment was conducted using STAR v.2.7.3a against Gencode (GRCh38 Release 34 primary assembly), counted using featureCounts, and differential expression was determined using DESeq2 v.1.28.1. A more detailed description is provided in the manuscript.
Please note that one of the raw files associated with the 'A375 Non-targetting Control Rep 2' sample is truncated (70414_1_1.fq.gz).

first: William

last: Giblin

first: Lauren

last: Bringman-Rodenbarger

first: Angela

last: Guo

first: Surinder

last: Kumar

first: Alexander

last: Monovich

first: Ahmed

last: Mostafa

first: Mary

last: Skinner

first: Michelle

last: Azar

last: Mady

first: Carolina

last: Chung

first: Namrata

last: Kadambi

first: Keith-Allen

last: Melong

first: Ho-Joon

last: Lee

first: Li

last: Zhang

first: Peter

last: Sajjakulnukit

first: Sophie

last: Trefely

first: Erika

last: Varner

first: Sowmya

last: Iyer

first: Min

last: Wang

first: James

last: Wilmott

first: H

last: Soyer

first: Richard

last: Sturm

first: Antonia

last: Pritchard

first: Aleodor

last: Andea

last: Scolyer

first: Mitchell

last: Stark

last: Scott

first: Douglas

middle: R

last: Fullen

first: Marcus

middle: W

last: Bosenberg

first: Sriram

last: Chandrasekaran

first: Zaneta

last: Nikolovska-Coleska

first: Monique

last: Verhaegen

first: Nathaniel

last: Snyder

first: Miguel

middle: N

last: Rivera

first: Andrei

last: Osterman

first: Costas


title: Identification of Corynebacterium diphtheriae manganese and MntR regulated genes

status: Public on May 06 2021

city: Silver Spring

first: Michael

last: Schmitt

address: 10903 New Hampshire Ave

institute: US Food and Drug Administration

summary:
We assessed changes in gene expression in response to manganese availability for the human pathogen Corynebacterium diphtheriae. Total RNA was harvested from wild-type C. diphtheriae strain 1737 and an isogenic ΔmntR (dip0619) grown in semi-defined metal-limited media (mPGT) without or with 5 µM manganese chloride supplementation. Three biological replicates were prepared and five genes were assessed by real-time PCR to validate the array results: dip0124, dip0169, dip0615, dip1923, and dip2261.
(Abstract) Corynebacterium diphtheriae is the causative agent of a severe respiratory disease in humans. The bacterial systems required for infection are poorly understood, but the acquisition of metals such as manganese (Mn) are likely critical for host colonization. MntR is a Mn-dependent transcriptional regulator in C. diphtheriae and was previously shown to repress the expression of the mntABCD genes, which encode an ABC metal transporter. However, other targets of Mn and MntR regulation in C. diphtheriae have not been identified. In this study, we use comparisons between the gene expression profiles of wild-type C. diphtheriae strain 1737 grown without or with Mn supplementation and comparisons of gene expression between wild-type and an mntR mutant to characterize the C. diphtheriae Mn and MntR regulon. MntR was observed to both repress and induce the expression of various target genes in a Mn-dependent manner. Genes induced by MntR include the Mn-superoxide dismutase, sodA, and the putative ABC transporter locus, iutABCD. DNA binding studies showed that MntR interacts at the promoter regions for several genes identified in the expression study, and a 17-bp consensus MntR DNA binding site was identified. We found that an mntR mutant displayed increased sensitivity to Mn and Cd that could be alleviated by the additional deletion of the mntA-D transport locus, providing evidence that the MntABCD transporter functions as a Mn uptake system in C. diphtheriae. The findings in this study further our understanding of metal uptake systems and global metal regulatory networks in this important human pathogen.

overall_design: Total RNA harvested from mid-logarithmic cultures of Corynebacterium diphtheriae strain 1737 (wild type and an isogenic mntR mutant). Both strains were grown under no and 5 µM manganese chloride supplementation in the semi-defined mPGT medium. Three separate cultures were used per strain and condition for a total of 12 samples.

first: Eric

last: Peng


title: Precise transcriptional control of cellular quiescence by BRAVO/WOX5 complex in Arabidopsis roots

city: Cerdanyola

first: Fidel

last: Lozano-Elena

state: Barcelona

address: Edifici CRAG - Campus UAB

department: Molecular Genetics

institute: Center for Research in Agricultural Genomics (CRAG)

summary: Understanding stem cell regulatory circuits is the next challenge in plant biology, as these cells are essential for tissue growth and organ regeneration in response to stress. In the Arabidopsis primary root apex, stem-cell specific transcription factors BRAVO and WOX5 co-localize in the Quiescent Center (QC) cells, where they commonly repress cell division so that these cells can act as a reservoir to replenish surrounding stem cells, yet their molecular connection remains unknown. Genetic and biochemical analysis indicates that BRAVO and WOX5 form a transcription factor complex that modulates gene expression in the QC cells to preserve overall root growth and architecture. Furthermore, by using mathematical modeling we establish that BRAVO uses the WOX5/BRAVO complex to promote WOX5 activity in the stem cells. Our results unveil the importance of transcriptional regulatory circuits in plant stem cell development.

overall_design: RNA-seq of QC cells of WT and bravo-2 Arabidopsis seedlings.

first: Isabel

last: Betegón-Putze

first: Ana

middle: I

last: Caño-Delgado

first: Rosangela

last: Sozzani


title: Niche stiffening compromises stem cell potential during aging by reducing chromatin accessibility at bivalent promoters

city: Münster

first: Sara

middle: A

last: Wickström

address: Röntgenstraße 20

department: Cell & Tissue Dynamics

country: Germany

institute: Max Planck Institute for Molecular Biomedicine

summary: RNA and ATAC sequencing data of CD34+ Ia6+ sorted hair follicle stem cells from 6 and 24 months old mice

overall_design:
Total RNA from 3 biological replicates of CD34+ Ia6+ sorted hair follicle stem cells from 6 and 24 months old mice . Paired-end sequencing 150bp reads HiSeq3000. ATAC-seq from 4 biological replicates of sorted hair follicle stem cells from 6 and 24 months old mice. Paired-end sequencing 75bp reads HiSeq4000.
H3K27me3 ChIP-seq from 3 biological replicates, and H3K4me3 and Pol2 ChIP-seq from 2 biological replicates of sorted hair follicle stem cells from 6 and 24 months old mice. Paired-end sequencing 100bp reads NovaSeq6000.


title: Loss of Smad4 promotes aggressive lung cancer metastasis by de-repression of PAK3 via miRNA regulation

city: Haining

first: Jian

last: Liu

state: Zhejiang

address: 718 East Haizhou Rd.

department: Zhejiang University - University of Edinburgh Institute

institute: Zhejiang University

summary: Over 85% of lung cancer patients harbor overt or subclinical metastases at diagnosis, and therefore most patients die of progressive metastatic disease despite aggressive local and systemic therapies. Somatic mutations in the Smad4 gene have been found in non-small-cell lung cancer, but the underlying mechanism by which Smad4 loss-of-function (LOF) accelerates lung cancer metastasis is yet to be elucidated. Here, we generated a highly aggressive lung cancer mouse model bearing conditional KrasG12D, p53fl/fl LOF and/or Smad4 fl/fl LOF mutations. The Smad4fl/fl; p53 fl/fl; KrasG12D (SPK) mutant mice manifested a much higher incidence of tumor metastases than the p53 fl/fl; KrasG12D (PK) mice. Molecularly, PAK3 was identified as a novel downstream effector of Smad4, mediating metastatic signal transduction via the PAK3-JNK-Jun pathway. Upregulation of PAK3 by Smad4 LOF in SPK mice was achieved by attenuating Smad4-dependent transcription of miR-495 and miR-543. These microRNAs (miRNAs) directly bind to the PAK3 3’UTR for blockade of PAK3 production, ultimately regulating lung cancer metastasis. An inverse correlation between Smad4 and PAK3 pathway components suggests clinical use of Smad4 LOF as a potential marker for prognosis in human lung cancer. Our study highlights the Smad4-PAK3 regulation as a point of potential therapy in metastatic lung cancer.

overall_design: In this study, we used adeno-Cre to conditionally activate a KrasG12D allele with concomitant deletion of Smad4 (Smad4 fl/fl) and p53 (p53fl/fl) genes to induce lung cancer. Expression of mutant KrasG12D along with p53 and Smad4 loss-of-function (LOF) engendered a high incidence of metastasis to different tissues, compared to that found in p53fl/fl; KrasG12D mice. We isolated lung tumors from Adeno-Cre - Smad4 fl/fl - p53 fl/fl - KrasG12D (SPK) mice and from Adeno-Cre - p53 fl/fl - KrasG12D (PK) mice, respectively. And then we conducted RNA-Seq analysis between SPK cells and PK cells.

first: Lei

last: Li

first: Dianwen

last: Song

first: Xiao

last: Yang

first: Xiaotao


title: Host-specific gene expression as a tool for introduction success in Naupactus parthenogenetic weevils

city: Wellesley

first: Andrea

last: Sequeira

state: MA

address: 106 Central St

department: Department of Biological Sciences

institute: Wellesley College

summary: Food resource access can mediate establishment success in invasive species, and generalist herbivorous insects are thought to rely on mechanisms of transcriptional plasticity to respond to dietary variation. While asexually reproducing invasives typically have low genetic variation, the twofold reproductive capacity of asexual organisms is a marked advantage for colonization. We studied host-related transcriptional acclimation in parthenogenetic, invasive, and polyphagous weevils: Naupactus cervinus and N. leucoloma. We analyzed patterns of gene expression in three gene categories that can mediate weevil-host plant interactions through identification of suitable host plants, short-term acclimation to host plant defenses, and long-term adaptation to host plant defenses and their pathogens. This approach employed comparative transcriptomic methods to investigate differentially expressed host detection, detoxification, immune defense genes, and pathway-level gene set enrichment. Our results show that weevil gene expression responses can be host plant-specific, and that elements of that response can be . Some host plant groups, such as legumes, appear to be more taxing as they elicit a complex gene expression response which is both strong in intensity and specific in identity. However, the weevil response to taxing host plants shares many differentially expressed genes with other stressful situations, such as host plant cultivation conditions and transition to novel host, suggesting that there is an evolutionarily favorable shared gene expression regime for responding to different types of stressful situations. Modulating gene expression in the absence of other avenues for phenotypic adaptation may be an important mechanism of successful colonization for these introduced insects.

sample_organism:
Naupactus cervinus
Naupactus leucoloma

platform_organism:
Naupactus cervinus
Naupactus leucoloma

overall_design: Analysis of differential gene expression in Naupactus weevil abdominal, head, and immature tissue under a variety of environmental conditions (e.g. host plant species, host plant cultivation technique) using RNA-seq.

first: Ava

last: Mackay-Smith

first: Mary

middle: K

last: Dornon

first: Rosalind

last: Lucier

first: Anna

last: Okimoto

first: Flavia

last: Mendonca de Sousa

first: Marcela

last: Rodriguero

first: Viviana

last: Confalonieri

first: Analia

last: Lanteri


title: The alarmin S100A9 hampers retroviral infection by limiting reverse transcription

city: Montpellier cedex 5

first: Fabien

last: Blanchet

address: 1919 route de Mende

institute: IRIM - CNRS UMR9004

summary: We identified the alarmin S100A9 as a novel intracellular antiretroviral factor expressed in human monocyte-derived and skin-derived Langerhans cells (LC). The expression of S100A9 is significantly upregulated by the transforming growth factor beta in human monocyte-derived cells. We showed that S100A9 intracellular expression is decreased upon maturation and inversely correlated with an enhanced inversely correlates with the maturation level of LC and susceptibilityility to HIV-1 infection of LC. Furthermore, silencing of S100A9 in primary human LC relieves HIV-1 restriction while ectopic expression of S100A9 in various cell lines established an intrinsic resistance to both HIV-1 and MMLV infection by acting on reverse transcription. Mechanistically, the intracellular expression of S100A9 alters viral capsid uncoating and reverse transcription in a distal manner. Also, S100A9 demonstrates potent inhibitory effect against HIV-1 and MMLV reverse transcriptase (RTase) activity in-vitro in a divalent cation-dependent context. Our findings uncover an unexpected intracellular antiretroviral function of the human alarmin S100A9 and highlight a novel crosstalk betweenregulating antiretroviral immunity in Langerhans cells

overall_design: Expression of TGF-beta regulated genes in various differentiated human primary monocyte-derived cells

first: Kyra

last: Fuchs

first: Laure

last: Papin

first: Ghizlane

last: Maarifi


title: Transcriptional reprogramming by oxidative stress occurs within a predefined chromatin accessibility landscape

city: Duluth

first: Matthew

last: Slattery

state: MN

address: 1035 University Drive, SMed 255

department: Biomedical Sciences

institute: University of Minnesota Medical School

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: TP53-mediated therapy-related clonal hematopoiesis contributes to doxorubicin-induced cardiomyopathy by augmenting a neutrophil-mediated cytotoxic response in a murine model

status: Public on May 05 2021

city: Charlottesville

first: Anupreet

last: Kour

state: Virginia

address: 415 Lane road

department: CVRC

institute: University of Virginia

summary: Therapy-related clonal hematopoiesis (t-CH) is often observed in cancer survivors. This form of clonal hematopoiesis typically involves somatic mutations in driver genes that encode components of the DNA damage response (DDR) and confer hematopoietic stem and progenitor cells (HSPC) with resistance to the genotoxic stress of the cancer therapy. A model of TP53-mediated t-CH was established through the transfer of Trp53-mutant HSPC to mice followed by treatment with a course of the chemotherapeutic agent doxorubicin. These studies revealed that neutrophil infiltration in the heart significantly contributes to doxorubicin-induced cardiac toxicity and that this condition is amplified in the model of Trp53-mediated t-CH. These data suggest t-CH could contribute to the elevated heart failure risk that occurs in cancer survivors.

overall_design: Peripheral blood neutrophils of Trp53-sufficient mice and Trp53- heterozygous deficient mice at 1 day after Dox injection (n=4 per genotype) were used for RNA isolation for sequencing.

first: Soichi

last: Sano

first: Ying

last: Wang

first: Hayato

last: Ogawa

first: Keita

last: Horitani

first: Miho

first: Ariel

last: Polizio

first: Yoshimitsu

last: Yura

first: Heather

last: Doviak

first: Kenneth

last: Walsh


title: TMEM41B is a host factor required for the replication of diverse coronaviruses including SARS-CoV-2

city: Durham

first: Nicholas

last: Heaton

state: NC

address: 213 Research Drive, 426 CARL Building

department: Molecular Genetics and Microbiology

institute: Duke University School of Medicine

summary: Identification of a host factor essential for coronavirus replication

overall_design: A CRISPR/Cas9 library was used to identify genes that rendered the cell refractory to killing by hCoV-229E. The complete sgRNA librarywas packaged into lentivirus and used to transduce Huh7 cells .  In two independent biological replicates, the transduced cells were infected with the virus, and the cells that were not killed by infection were collected and the sgRNAs enriched in those populations were sequenced.

first: Joseph

last: Trimarco


title: c-Myc targeted genes validated by PCR array in STEAP1-silenced HepG2 cells.

city: Sapporo

first: Hajime

last: Nakamura

state: Hokkaido

address: South-1, West-16, Chuo-ku

department: Department of Medical Oncology

institute: Sapporo Medical University School of Medicine

summary: To confirm the relationship between STEAP1 and c-Myc in liver cancer, we analyzed components of c-Myc-related genes after STEAP1 knockdown in HepG2 cells by PCR array.

overall_design: There are two groups: siSTEAP1 and Control.


title: An integrative analysis of genome-wide 5-hydroxymethylcytosines in circulating cell-free DNA detects non-invasive diagnostic markers for gliomas

status: Public on May 30 2021

city: Chicago

first: Wei

last: Zhang

state: IL

address: 680 N Lake Shore Drive, Suite 1400

department: Preventive Medicine

institute: Northwestern University

summary:
Background. Gliomas, especially the high-grade glioblastomas (GBM), are highly aggressive tumors in the central nervous system (CNS) with dismal clinical outcomes. Effective biomarkers, which are not currently available, may improve clinical outcomes through early detection. We sought to develop a non-invasive diagnostic approach for gliomas based on 5-hydroxymethylcytosines (5hmC) in circulating cell-free DNA (cfDNA).
Methods. We obtained genome-wide 5hmC profiles using the 5hmC-Seal technique in cfDNA samples from 111 prospectively enrolled patients with gliomas and 111 age-, gender-matched healthy individuals, which were split into a training set and a validation set. Integrated models comprised of 5hmC levels summarized for gene bodies, long non-coding RNAs (lncRNAs), cis-regulatory elements, and repetitive elements were developed using the elastic net regularization under a case-control design.
Results. The integrated 5hmC-based models differentiated healthy individuals from gliomas (AUC [area under the curve] = 84%; 95% confidence interval [CI], 74-93%), GBM patients (AUC = 84%; 95% CI, 74-94%), WHO II-III glioma patients (AUC = 86%; 95% CI, 76-96%), regardless of IDH1 (encoding isocitrate dehydrogenase) mutation status or other glioma-related pathological features such as TERT, TP53 in the validation set. Furthermore, the 5hmC biomarkers in cfDNA showed the potential as an independent indicator from IDH1 mutation status and worked in synergy with IDH1 mutation to distinguish GBM from WHO II-III gliomas. Exploration of the 5hmC biomarkers for gliomas revealed relevance to glioma biology.
Conclusions. The 5hmC-Seal in cfDNA offers the promise as a non-invasive approach for effective detection of gliomas in a screening program.

first: Jiajun

last: Cai

first: Chang

last: Zeng

last: Hua

first: Zengxin

last: Qi

first: Yanqun

last: Song

first: Xingyu

last: Lu

first: Zhou

first: Xin

first: Zixiao

last: Yang

first: Jinsen

first: Kai

last: Quan

last: Zhu

first: Jiabin

first: ShiYuan

last: Cheng

first: Chuan

last: He

last: Mao

first: Dongdong

last: Li

first: Xiaolong

last: Cui


title: iPSC-endothelial cell phenotypic drug screening and in silico analyses identify tyrphostin AG1296 for pulmonary arterial hypertension

city: Cincinnati

first: Minzhe

last: Guo

state: OH

address: 3333 BURNET AVENUE

department: Pulmonary Biology

institute: Cincinnati Children's Hospital Medical Center

summary: Pulmonary arterial hypertension (PAH) is a progressive disorder leading to occlusive vascular remodeling. Current PAH therapies improve quality of life but do not reverse structural abnormalities in the pulmonary vasculature. Here, we used a high-throughput drug screen combined with in silico analyses of existing transcriptomic datasets to identify a promising lead compound to reverse PAH. Induced pluripotent stem cell-derived endothelial cells (iPSC-EC) generated from six patients with PAH were exposed to 4,500 compounds and assayed for improved cell survival after serum withdrawal using a chemiluminescent caspase assay. Subsequent validation of caspase activity and improved angiogenesis combined with in silico analyses using the Gene Expression Omnibus (GEO ) and Library of Integrated Network-Based Cellular Signatures (LINCS) databases revealed that the lead compound AG1296 was positively associated with an anti-PAH gene signature. AG1296 increased abundance of bone morphogenetic protein receptors (BMPR2 and Ia), downstream signaling and gene expression, and suppressed PAH smooth muscle cell proliferation. AG1296 induced regression of pulmonary arterial (PA) neointimal lesions in lung organ culture and PA occlusive changes in the Sugen/hypoxia rat model and reduced right ventricular systolic pressure. Moreover, AG1296 improved vascular function and BMPR2 signaling and showed better correlation with the anti-PAH gene signature than other tyrosine kinase inhibitors (TKIs) such as imatinib. Specifically, AG1296 upregulated the transcription factors and small mothers against decapentaplegic (SMAD)1/5 co-activators, cAMP-response element binding protein (CREB)3 and CREB5: CREB3 induced inhibitor of DNA binding 1 (ID1)  and downstream genes that improved vascular function. Thus, drug discovery for PAH can be accelerated by combining a phenotypic screen using patient-specific iPSC-derived vascular cells with in silico analyses of publicly available datasets.

overall_design:
mRNA from endothelial cells derived from iPSCs, primary pulmonary artery endothelial cells, and primary pulmonary artery smooth muscle cells from 6 patients with PAH. All treated with or without AG1296.
**RAW data will be submitted to dbGAP**

first: Mingxia

last: Gu

first: Michele

last: Donato


title: The nature of the second hit defines tumor cell identity during developmental susceptibility to leukemia-associated ETV6-RUNX1

city: Homburg (Saar)

first: Marc

last: Remke

state: Saarland

address: Kirrberger Straße 100, Gebäude 9

department: Pediatric Translational Oncology Lab

institute: Universitätsklinikum des Saarlandes

summary: ETV6-RUNX1 is associated with childhood B-cell acute lymphoblastic leukemia (B-ALL), but the consequence of ETV6-RUNX1 expression on cell lineage decision during B-cell leukemogenesis remains largely evasive. Clinically silent ETV6-RUNX1 preleukemic clones are frequently found in neonatal cord blood, but only a few carriers develop B-ALL as a result of the acquisition of secondary postnatal genetic hits, like KDM5C or PAX5 loss. However, understanding the mechanism involved in this transformation would advance the development of non-toxic prophylactic interventions to preleukemic carriers. Using genetic lineage tracing, we have examined the capacity of ETV6-RUNX1 in instructing a B-cell malignant phenotype. Restricted Cre-mediated activation of ETV6-RUNX1 from the endogenous Etv6 locus into B-cell precursors does not trigger B-ALL development. Similarly, concomitant transient ETV6-RUNX1 expression in hematopoietic progenitors close to restricted Cre-mediated introduction of second hit (Kdm5c loss) in B-cells fail to induce B-ALL. In contrast, targeting ETV6-RUNX1 in hematopoietic progenitors was required to induce leukemia. These mice develop either T-ALL or B-ALL, suggesting that the nature of the second hit may define tumor cell identity during ETV6-RUNX1 leukemogenesis.   In order to uncover a potential exclusive effect of the second hit in establishing the leukemic phenotype, we next showed that the introduction of the second hit, either Kdm5c or Pax5 loss, to the ETV6-RUNX1 preleukemic clone confers the tumor B-cell identity without need of environmental infection exposure. The resulting B-ALLs clustered according to the second-hit by RNA sequencing (RNA-Seq) analysis. Together these results provide a novel paradigm for the generation of tumor B cells through ETV6-RUNX1 in vivo where the second hit confers the tumor cell-identity to the ETV6-RUNX1 preleukemic clone. These findings could be relevant to develop new therapeutic approaches to prevent disease development.

overall_design: Analysis of B-and T-ALL from different genetic mouse backgrounds

first: Daniel

last: Picard

first: Isidro

last: Sanchez-Garcia


title: Characterization of in vitro cultured alveolar macrophages (AM) transcriptomes and heterogeneity following Wnt3a treatment

city: Rochester

first: Bibo

address: 200 1st ST SW

department: Pulmonary and Critical Care Medicine

institute: Mayo Clinic


title: Transcriptomic changes in the interaction between PCL1606 and FZB42

city: Malaga

first: Carlos

middle: Molina

last: Santiago

state: Malaga

address: Bulevar Louis Pasteur 49

department: MIcrobiology

institute: UMA

summary: We report the application of a high-throughput technique, RNA-seq, to study the transcriptomic response of P. chlororaphis and Bacillus amyloliquefaciens growing in co-cultures in King B solid medium

sample_organism:
Bacillus amyloliquefaciens
Pseudomonas chlororaphis

overall_design: Single colonies of PCL1606 and FZB42 WT and the GlpK mutant were grown overnight in LB medium at 30°C. Overnight cultures were diluted to a starting OD600 of 0.01 in the same medium and 2 µl were spotted on King B plates alone and in interaction between PCL1606 and the Bacillus strains.

first: C

last: Molina-Santiago

first: D

last: Romero


title: Characterization of in vitro cultured alveolar macrophages (AM) transcriptomes [bulk RNA-seq]

summary: To identify molecular characteristics of WT AM without Wnt3a, and WT, b-catenin-deficient or HIF-1a-deficient AM with Wnt3a stimulation in vitro, we isolated RNA from AMs with various treatments and examined by bulk RNA-seq. We found a large number of gene profiles were altered following Wnt3a treatment in WT AMs, while b-catenin and HIF-1a deficiency largely abolished the effects of Wnt3a treatment on AM transcription, suggesting that b-catenin and HIF-1a mediates most downstream effects of Wnt3a in AMs. Indeed,HIF-1a-deficient AMs essentially phenocopied those of b-catenin-deficient AMs, with more than 80% of differentially expressed genes in HIF-1a-deficient AMs overlapping with b-catenin-deficient AMs following Wnt3a treatment.

overall_design: Examined with bulk WT, b-catenin-deficient or HIF-1a-deficient AM treated with or without Wnt3a in vitro for overnight

first: Yue

last: Wu

first: Jie

last: Sun


title: Epigenome analysis of parental (native) and 3-bromopyruvate-resistant UM-UC-3 bladder cancer cells

status: Public on May 04 2021

city: Brussels

first: Cyril

last: Corbet

state: Select State/Prov.

address: Avenue Hippocrate 57

department: Institut de Recherche Expérimentale et Clinique (IREC)

institute: UCLouvain

type: Methylation profiling by genome tiling array

summary: Genome-wide DNA methylation profiling of parental (native) and 3-bromopyruvate-resistant UM-UC-3 bladder cancer cells. The Illumina Infinium 450k Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 450,000 CpGs in treatment-naive and 3-bromopyruvate-resistant UM-UC-3 bladder cancer cells.

overall_design: Bisulphite-converted DNA from the 12 samples were hybridized to the Illumina Infinium 450k Human Methylation Beadchip v1.2

first: Olivier

last: Feron


title: Characterization of in vitro cultured alveolar macrophages (AM) heterogeneity following Wnt3a treatment [single-cell RNA-seq]

last: Zhu

summary: To understand how Wnt signaling affects AM phenotype in vitro, we treated AMs pooled from 5 WT mice with or without Wnt3a for overnight and performed single-cell RNA sequencing analysis in the cells. Dimensionality reduction analysis of combined control or Wnt3a-treated AMs revealed eight clusters based on their gene expression pattern, and control or Wnt3a-treated AMs were almost mutually exclusive as visualized in UMAP plot.

overall_design: Examined with control or Wnt3a-treated AMs cultured in vitro.


title: Core liver homeostatic co-expression networks are preserved between mouse and human but respond to perturbations in an organism- and disease-specific manner

city: Sydney

first: Saeed

last: Esmaili

state: NSW

address: 176 Hawkesbury Rd, Westmead

department: Storr Liver Centre

country: Australia

institute: Westmead Institute for Medical Research

summary: Chronic complex diseases are difficult to model in animals and to reproducibly translate the findings to human disease. We argued that organs have core networks that are preserved between species and are predictably altered when homeostasis is disrupted. We altered hepatic homeostasis in mice by dietary challenge and compared the liver transcriptome to that in metabolic associated fatty liver disease (MAFLD) and liver cancer.

overall_design: Total liver RNA was extracted using RNAeasy (Qiagen). RNA purity and integrity were confirmed using an Agilent Bioanalyzer. Libraries were prepared from 100 ng total RNA (TruSeq Stranded Total RNA kit, Illumina) and singled-ended sequencing performed on the Illumina HiSeq 2500 using bar-coded multiplexing and a 50 bp read length, yielding a median of 10.7 M reads per sample. Read alignment and junction finding was accomplished using STAR using the ‘quantmode GeneCounts’ option and an Ensemble mm10 annotation in GTF format.

first: Christopher

last: Liddle


title: Host-dependent Phenotypic Resistance to EGFR Tyrosine Kinase Inhibitors

city: Rehovot

first: Yosef

last: Yarden

address: Herzl St 234

department: Biological Regulation

country: Israel

institute: Weizmann Institute of Science

summary: RNA-Seq comparison of Dacomitinib resistant PC9 lung adenocarcinoma cells vs the parental cells.

overall_design: PC9 cells were treated with increasing concentration of dacomitinib (from 1 pM to 100 nM) for 6 months. Dacomitinib resistant cells treated with Dacomitib (100 nM) were compared to the Parental PC9 cells.

first: Diana

last: Drago

first: Yossi

first: Yuya

last: Haga

first: Arunachalam

last: Sekar


title: CRISPR screen identifies NUDT21 as a regulator of intron detention of the SAM synthetase MAT2A RNA

city: Dallas

first: Nicholas

last: Conrad

address: 6000 Harry Hines Blvd

department: Microbiology

institute: UT Southwestern Medical Center

summary: The only S-adenosymethionine (SAM) synthetase expressed in most human cells, MAT2A, is regulated by intron detention. Using a GFP fusion reporter, we conducted a CRISPR screen to identify regulators of this alternative splicing event. The screen identified METTL16, a known regulator of this process, and NUDT21. NUDT21 encodes the CFIm25 protein a member of the CFIm complex involved in alternative polyadenylation. Validation and follow-up studies support the idea that CFIm25 and the larger CFIm complex plays an unanticipated role in splicing of the MAT2A detained intron.

overall_design: We generated a GFP reporter containng the MAT2A detained intron that responds to SAM depletion by increasing splicing, and therefore GFP signal. Using the Brunello knockout CRISPR lentivirus library (Doench et al. 2016; Addgene #73179), we looked for genes that were necessary for GFP induction upon SAM depletion. We performed three replicates of the screen and compared the sgRNAs found in sorted cells (those with low GFP signal) to sgRNAs found in the unselected pool of cells. In the data below, the samples called "sort2-4" are the selected cells and the unselected control are referred to as the "input2-4". The sequencing data were then analyzed by MAGeCK (Li et al. 2014).

first: Anna

middle: M

last: Scarborough

first: Ashwani

last: Kumar

first: Chao

last: Xing


title: SET1B facilitates activation of the hypoxia response through site-specific histone methylation

city: Cambridge

first: James

last: Nathan

address: Jeffrey Cheah Biomedical Centre

department: Medicine

country: United Kingdom

institute: University of Cambridge

summary: Hypoxia-inducible transcription factors (HIFs) are fundamental to the cellular adaptation to low oxygen levels but how they interact with chromatin and efficiently activate their target genes is unclear. Using genome-wide mutagenesis in human cancer cells, we define genes required for HIF transcriptional activation, and identify a requirement for the Histone 3 lysine 4 (H3K4) methyltransferase SET1B. Loss of SET1B leads to a selective reduction in HIF transcriptional activity in hypoxia, with SET1B driving expression of genes involved in angiogenesis rather than glycolysis, resulting in impaired tumour establishment in SET1B deficient xenografts.  Mechanistically, we show that SET1B is itself oxygen regulated, accumulates on chromatin in hypoxia, and is recruited to HIF target genes through HIF-1a. Accordingly, we show that the hypoxic induction of H3K4me3 at specific HIF targets is both HIF and SET1B dependent, and when impaired, decreases promotor acetylation and gene expression. Together, these findings reveal SET1B as a determinant of site-specific histone methylation and provide insight into how HIF target genes are differentially regulated.

overall_design: We used RNA-seq to determine gene expression in HeLa cells, HIF1b deficient HeLa cells or SET1B deficient HeLa cells incubated in 21% or 1% oxygen for 12 hr

first: Brian

last: Ortmann


title: Comparison of spatial sequencing in leprosy lesions from lepromatous and reversal reaction patients

city: Los Angeles

first: Feiyang

last: Ma

state: CA

address: 610, Charles Young Dr East, TLSB 3000C

department: Molecular Biology Institute

institute: UCLA

summary: Granulomas are complex cellular structures comprised predominantly of macrophages and lymphocytes that function to contain and kill invading pathogens. Here, we investigated single cell phenotypes associated with antimicrobial responses in human leprosy granulomas by applying single cell and spatial sequencing to leprosy biopsy specimens. We focused on reversal reactions (RR), a dynamic process in which some patients with disseminated lepromatous leprosy (L-lep) transition towards self-limiting tuberculoid leprosy (T-lep), mounting effective antimicrobial responses. We identified a set of genes encoding proteins involved in antimicrobial responses that are differentially expressed in RR versus L-lep lesions, and regulated by IFN- and IL-1. By integrating the spatial coordinates of the key cell types and antimicrobial gene expression in RR and T-lep lesions, we constructed a map revealing the organized architecture of granulomas depicting compositional and functional layers by which macrophages, T cells, keratinocytes and fibroblasts contribute to the antimicrobial response.

overall_design: Examine differences between Lepromatous and Reversal reaction lesions by spatial sequencing

first: Olesya

last: Plazyo

first: Johann

last: Gudjonsson

first: Matteo

last: Pellegrini

first: Robert

middle: L

last: Modlin


title: Changes in bacterial diversity and composition detected in plasma determine immunological outcome in HIV+ persons initiating antiretroviral therapy

city: Atlanta

first: Rafick-Pierre

last: Sekaly

state: GA

address: 1750 Haygood Drive

department: Pathology

institute: Emory University

summary: The impact of the microbiome on HIV disease is widely acknowledged although the mechanisms downstream of fluctuations in microbial composition remain speculative. We detected rapid, dynamic changes in translocated microbial constituents during two years after cART initiation. An unbiased systems biology approach revealed two distinct pathways driven by changes in the abundance ratio of Serratia to other bacterial genera. Increased CD4 T cell numbers over the first year were associated with high Serratia abundance, pro-inflammatory innate cytokines, and metabolites that drive Th17 gene expression signatures and restoration of mucosal integrity. Subsequently, decreased Serratia abundance and downregulation of innate cytokines allowed re-establishment of systemic T cell homeostasis promoting restoration of Th1 and Th2 gene expression signatures. Analyses of three other geographically distinct cohorts of treated HIV infection established a more generalized principle that changes in diversity and composition of translocated microbial species influence systemic inflammation and consequently CD4 T cell recovery.

sample_organism:
Homo sapiens
human blood metagenome

platform_organism:
Homo sapiens
human blood metagenome

overall_design: Primary cohort: A total of 11 treatment-naive HIV-infected individuals were recruited at the Joint Clinical Research Center (JCRC) in Kampala Uganda. All participants had detectable plasma HIV viremia and no prior antiretroviral therapy (ART). Combination ART was started at baseline with blood samples collected longitudinally (at months 0, 3, 4, 9, 12 and 24) for pathogen sequencing and immune cell subset RNA sequencing (sorted monocytes and T cells at months 0, 3, 12, 24). Secondary cohorts: Plasma sample collection and pathogen sequencing were done on three independent HIV cohorts with a total of 109 participant timepoints with known T cell counts were assessed in our study. The second Ugandan cohort consisted of 7 HIV uninfected, 10 HIV-infected on cART and 3 paired HIV-infected off cART. The Montreal cohort (Morou et al., 2019) consisted of 6 HIV uninfected and 28 HIV-infected, of which 5 were elite controllers, 3 viremic progressors of which 1 with a paired post-cART timepoint, 12 chronic progressors pre-cART of which 8 with paired post-cART timepoint. The Cleveland cohort (Lederman et al., 2011) consisted of HIV-infected persons on cART, with 11 immune responders and 44 immune non-responders. Across cohorts, cART participant timepoints were 1-3 years post treatment initiation.

first: Krystelle

last: Nganou-Makamdop

first: Aarthi

last: Talla

first: Ashish

last: Sharma

first: Sam

last: Darko

first: Daniel

last: Douek


title: Transcriptome analysis of mouse preimplantation embryos when DNA damage checkpoint is perturbed

city: Beijing

first: Ting

last: WANG

address: Qinghuayuan Street

institute: Tsinghua University

summary: To investigate the importance of DNA damage checkpoint regulation in mammalian preimplantation embryos, we overexpressed wild type and mutant form of CHK1 kinase in mouse zygotes and performed high-throughput RNA-sequencing  of zygotes,  late 2-cell embryos and blastocysts. Transcriptome analysis revealed that zygotes are particular sensitive to the perturbation of Chk1 governed DNA damage checkpoint. However, once zygotes can overcome DNA damage checkpoint induced cell cycle arrest, they can still have normal development.

overall_design: Microinjection of mRNA encoding wt and mutant CHK1 in early mouse zygotes, then treat with or without Chk1 inhibitor for short-term, then perform high-throughput RNA-sequencing  of zygotes,  late 2-cell embryos and blastocysts.

first: Jie

last: Wang

first: Jianying

last: Guo


title: NUDT21 regulates intron detention of the SAM synthetase MAT2A RNA

first: Nicholas

last: Conrad

state: TX

summary: NUDT21 encodes the CFIm25 protein, a component of the CFIm complex that regulates alternative polyadenylation (APA). Our data suggest that the CFIm complex also induces splicing of a detained intron in the the S-adenosylmethionine (SAM) synthetase MAT2A to control intracellular levels of SAM. To genetically separate these functions, we used poly(A) Click-seq (PAC-seq) to determine the changes in poly(A) site selection in two cell lines. The parental cell line is the colorectal cell line HCT116 and a derivative line that has the detained intron of MAT2A  deleted in both alleles of MAT2A (116-DDI). We found few differences in alternative polyadenylation after CFIm25 depletion were similar supporting teh conclusion that CFIm's role in APA is mechanistically distinct from its role in regulation of MATA splicing.

overall_design: We used siRNAs to knockdown NUDT21/CFIm25 expression for four days in either the parental HCT116 cell line or in 116-ΔDI cells. A nontargeting (NT) siRNA was used as a control. We then performed PAC-seq with ClickSeq Technologies (Galveston, TX) to analyze changes in APA. Three independent biological replicates were performed.

first: Anna

last: Scarborough


title: Comparison of single cell RNA sequencing in leprosy lesions from lepromatous and reversal reaction patients

summary: we performed single-cell RNA-sequencing by Seq-Well on skin biopsy specimens from five reversal and five lepromatous patients. We obtained 21,318 cells from 10 biopsy specimens, detecting an average of 741 genes and 3,556 transcripts per cell. we recovered 12 primary cell types across all 10 samples. These annotated cell types include: T cells, B cells, plasma cells, myeloid cells, Langerhans cells, mast cells, keratinocytes, fibroblasts, smooth muscle cells, endothelial cells, eccrine gland cells and melanocytes.

overall_design: Examine differences between Lepromatous and Reversal reaction lesions

first: Travis

last: Hughes


title: Multi-tissue Single-Cell Analysis Deconstructs the Complexities of Mouse NK-ILC1 Programs

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

summary: Natural killer (NK) cells and type 1 innate lymphoid cells (ILC1s) are a heterogenous group of T-bet+ innate cells that produce IFN-γ and are broadly defined as lineage–NK1.1+NKp46+ cells in mice. ILC1s definition primarily stems from studies on liver-resident and small intestinal populations. However, ILC1s in many anatomical sites, including visceral adipose tissue, salivary glands, and uterus, exhibit non-uniform programs that do not adequately overlap with those of liver or gut ILC1s or NK cells. Here, we performed single-cell RNA sequencing on murine NK1.1+NKp46+ cells from blood, spleen, lymph nodes, liver, salivary gland, uterus, visceral adipose tissue, small intestines, and several solid tumors. By including cells from an array of niches we defined tissue-specific ILC1 subsets. Moreover, we found a significant heterogeneity of circulating NK cells, due to a spectrum of proliferating, effector and migration programs, which was reduced in tumor-bearing mice, demonstrating repertoire reshaping in response to diseased conditions.

overall_design: NK/ILC1 cells (NK1.1+,NCR1+<Lin-) cells are collected from different tissues of WT or tumor-bearing C57BL/6 animals. Cells are sorted and single cell library of tissue-specific NK cells is sequenced.

first: Adelle

middle: P

first: Adam

last: Jelinski

first: Shuang-Yin

first: Victor

last: Cortez

first: Tomer

last: Landsberger

first: Hannah

last: Miller

first: Biancamaria

last: Ricci

first: Eyal

last: David

first: Roberta

last: Faccio

first: Marco

last: Colonna


title: Regulation network of colorectal cancer specific enhancers in progression of colorectal cancer

status: Public on May 03 2021

city: Tianjin

first: Bohan

last: Chen

address: NO.94 Weijin Road

institute: Nankai University

summary: Enhancers regulate multiple genes through higher-order chromatin structure and further affect cancer progression. Epigenetic changes in cancer cells activate several cancer specific enhancers that are silenced in normal cells. These cancer specific enhancers are potential therapeutic targets of cancer. However, functions and regulation network of colorectal cancer specific enhancers are still unknown. Here in this study, we profile colorectal cancer specific enhancers and reveal the regulation network of these enhancers by analysis of HiChIP, Hi-C and RNA-seq data. We propose the regulation network of colorectal cancer specific enhancers plays important role in progression of colorectal cancer.

overall_design: colorectal cancer cell lines, HCT116 were performed with HiChip including 2 replicates

first: Lei

last: Zhang


title: Characterizing the tumor microenvironment of metastatic ovarian cancer by single cell transcriptomics

first: Bingqing

last: Xie

state: Texas

address: 6001 Forest Park Rd

department: Internal medicine

institute: University of Texas Southwestern medical center

summary: Understanding the cellular composition of the tumor microenvironment and the interactions of the cells is essential to the development of successful immunotherapies in cancer. We perform single-cell RNA sequencing (scRNA-seq) of 9,885 cells isolated from the omentum in 6 patients with ovarian cancer and identify 9 major cell types, including cancer, stromal, and immune cells. Transcriptional analysis of immune cells stratifies our patient samples into 2 groups: (1) high T cell infiltration (high Tinf) and (2) low T cell infiltration (low Tinf). TOX-expressing resident memory CD8+ T (CD8+ Trm) and granulysin-expressing CD4+ T cell clusters are enriched in the high Tinf group. Concurrently, we find unique plasmablast and plasma B cell clusters, and finally, NR1H2+IRF8+ and CD274+ macrophage clusters, suggesting an anti-tumor response in the high Tinf group. Our scRNA-seq study of metastatic tumor samples provides important insights in elucidating the immune response within ovarian tumors.

overall_design: scRNA-seq of ovarian cancer metastatic cells from six ovarian cancer patients

first: Susan

last: Olalekan

first: Rebecca

last: Back

first: Heather

last: Eckart

first: Anindita

last: Basu


title: MicroRNA-seq of MDA-MB-231 cells transduced with anti-ELOVL5 and control shRNAs

city: Moscow

first: Stepan

last: Nersisyan

address: Vavilova str 7

department: Faculty of Biology and Biotechnology

country: Russia

institute: HSE University

type: Non-coding RNA profiling by high throughput sequencing

summary: MiRNA isoforms (isomiRs) are single stranded small RNAs originating from the same pri-miRNA hairpin as a result of cleavage by Drosha and Dicer enzymes. Variations at the 5’-end of a miRNA alter the seed region of the molecule, thus affecting the targetome of the miRNA. MDA-MB-231 cells were transduced with shRNAs against ELOVL5 and luciferase genes. Small RNA sequencing was used to study the cleavage profiles of shRNAs.

overall_design: Sequencing was performed for two samples: MDA-MB-231 cells trancduced with shELOVL5 and MDA-MB-231 cells trancduced with shLuc.

first: Anton

last: Zhiyanov

first: Alexander

last: Tonevitsky


title: Dynamic miRNA-mRNA regulations are essential for maintaining Drosophila immune homeostasis during Micrococcus luteus infection

city: Nanjing

first: Hongjian

last: Zhou

address: No.1 Wenyuan Road, Xianlin University Town, Nanjing

institute: Nanjing Normal University

summary: Pathogen bacteria infections can lead to dynamic changes of microRNA (miRNA) and mRNA expression profiles, which may control synergistically the outcome of immune responses. To reveal the role of dynamic miRNA-mRNA regulation in Drosophila innate immune responses, we have detailedly analyzed the paired miRNA and mRNA expression profiles at three time points during Drosophila adult males with Micrococcus luteus (M. luteus) infection using RNA- and small RNA-seq data. Our results demonstrate that differentially expressed miRNAs and mRNAs represent extensively dynamic changes over three time points during Drosophila with M. luteus infection. The pathway enrichment analysis indicates that differentially expressed genes are involved in diverse signaling pathways, including Toll and Imd as well as orther signaling pathways at three time points during Drosophila with M. luteus infection. Remarkably, the dynamic change of miRNA expression is delayed by compared to mRNA expression change over three time points, implying that the "time" parameter should be considered when the function of miRNA/mRNA is further studied. In particular, the dynamic miRNA-mRNA regulatory networks have shown that miRNAs may synergistically regulate gene expressions of different signaling pathways to promote or inhibit innate immune responses and maintain homeostasis in Drosophila, and some new regulators involved in Drosophila innate immune response have been identified. Our findings strongly suggest that miRNA regulation is a key mechanism involved in fine-tuning cooperatively gene expressions of diverse signaling pathways to maintain innate immune response and homeostasis in Drosophila. Taken together, the present study reveals a novel role of dynamic miRNA-mRNA regulation in immune response to bacteria infection, and provides a new insight into the underlying molecular regulatory mechanism of Drosophila innate immune responses.

overall_design: the injured PBS and infected M. luteus male adult flies were collected at 3 h, 12 h and 24 h post-infection for subsequently RNA-seq

first: Fei

last: Ma

first: Guanyun

last: Wei

first: Ruimin

last: Li


title: Deciphering mesenchymal drivers of human Dupuytren’s disease at single-cell level

city: Edinburgh

first: John

middle: Roger

last: Wilson-Kanamori

address: 47 Little France Crescent

department: Centre for Inflammation Research

institute: University of Edinburgh

summary: Dupuytren’s disease (DD) is a common, progressive fibroproliferative disease affecting the palmar fascia of the hands, causing fingers to irreversibly flex towards the palm with significant loss of function. Surgical treatments are limited, therefore effective new therapies for DD are urgently required. To identify key cellular and molecular pathways driving DD we employed single-cell RNA sequencing (scRNA-seq), profiling the transcriptomes of 35,250 human single cells from DD, non-pathogenic fascia, and healthy dermis. We identify a DD-specific population of pathogenic PDPN+/FAP+ mesenchymal cells displaying elevated expression of fibrillar collagens and profibrogenic genes. In silico trajectory analysis reveals resident fibroblasts to be the source of this pathogenic population. To resolve the processes governing DD progression, genes differentially expressed during fibroblast differentiation were identified including upregulated TNFRSF12A and transcription factor SCX. Knockdown of SCX and blockade of TNFRSF12A inhibited proliferation and altered pro-fibrotic gene expression of cultured human FAP+ mesenchymal cells, demonstrating a functional role for these genes in DD. The power of scRNA-seq is utilised to identify the major pathogenic mesenchymal subpopulations driving DD and key molecular pathways regulating the DD-specific myofibroblast phenotype. Using this precision medicine approach, inhibition of TNFRSF12A has shown potential clinical utility in the treatment of Dupuytren’s disease.

overall_design: Single, live cells were isolated from DD tissue, non-pathogenic fascia (from the transverse ligament of the palmar aponeurosis, herein referred to as Skoog’s fascia), and healthy dermis (n=3 DD, n=3 Skoog’s fascia, and n=3 healthy dermis). All tissue was taken at the time of corrective surgery for DD.

first: Ross

last: Dobie

first: Chris

middle: C

last: West

first: Beth

last: Henderson


title: Targeting bacterial gyrase with cystobactamid, fluoroquinolone and aminocoumarin antibiotics induces distinct molecular signatures in Pseudomonas aeruginosa

city: Braunschweig

first: Raimo

last: Franke

state: Lower Saxony

address: Inhoffenstr. 7

department: Chemical Biology

institute: Helmholtz Centre for Infection Research

summary: The design of novel antibiotics that break antimicrobial resistance relies on a profound understanding of their mechanism of action. While it has been shown that the cellular effects of antibiotics cluster according to their molecular targets, we investigated whether compounds binding to different sites of the same target can be differentiated by their transcriptome or metabolome signatures. The effects of three fluoroquinolones, two aminocoumarins and two cystobactamids, all inhibiting bacterial gyrase, on Pseudomonas aeruginosa at sub-inhibitory concentrations were captured by RNA sequencing.

overall_design: RNASeq of Pseudomonas aeruginosa PA14 treated with gyrase inhibitors from three different classes and untreated control- planctonic growth in BM2 medium.

first: Heike

last: Overwin

first: Susanne

last: Häussler

first: Mark

last: Brönstrup


title: Transcriptome analysis of zebrafish, medaka and zebraka chimeras

city: Sevilla

first: Lorena

last: Buono

state: Sevilla

address: Carretera de Utrera km 1

institute: CABD

summary: Transplanted zebrafish blasstomeres into a medaka host develop into a retina that expresses retinal genes

sample_organism:
Danio rerio
Oryzias latipes

platform_organism:
Danio rerio
Oryzias latipes

overall_design: Entire embryos and chimeras were used to extract total RNA that was sent for RNA-seq.

first: Lazaro

last: Centanin


title: Long noncoding RNA MIR4435-2HG enhances metabolic function of myeloid dendritic cells from HIV-1 elite controllers (Cut&Run)

first: Ce

last: Gao

state: MA

address: 400 Technology Square

institute: Ragon Institute of MGH, MIT and Harvard

summary: Restriction of HIV-1 replication in elite controllers (ECs) is frequently attributed to T cell-mediated immune responses, while the specific contribution of innate immune cells is less clear. Here, we demonstrated an upregulation of the host long non-coding RNA (lncRNA) MIR4435-2HG in primary myeloid dendritic cells (mDc) from ECs. Elevated expression of this lncRNA in mDCs was associated with a distinct immunometabolic profile, characterized by increased oxidative phosphorylation and glycolysis activities in response to TLR3 stimulation. Using functional assays, we showed that MIR4435-2HG directly influenced the metabolic state of mDCs, likely through epigenetic mechanisms involving H3K27ac enrichment at an intronic enhancer in the RPTOR gene locus, the main component of the mammalian target of rapamycin complex 1 (mTORC1). Together, these results suggested a role of MIR4435-2HG for enhancing immunometabolic activities of mDCs in ECs through targeted epigenetic modifications of a member of the mTOR signaling pathway.

overall_design: We performed CUT&RUNseq on myeloid DCs from PBMCs of four HIV-1 Elite controllers and four HIV-1 negative individuals to prolife histone modifications in the genomic regions.

first: Ciputra

last: Hartana

first: Yelizaveta

last: Rassadkina

first: Enrique

last: Martin-Gayo

first: Bruce

middle: D

last: Walker

first: Mathias

last: Lichterfeld

first: Xu

last: Yu


title: Long noncoding RNA MIR4435-2HG enhances metabolic function of myeloid dendritic cells from HIV-1 elite controllers

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Intratumoral TFR cells curtail anti-PD-1 treatment efficacy [mouse]

city: La Jolla

first: Pandurangan

last: Vijayanand

state: California

address: 9420 Athena Circle

department: Division of Vaccine Discovery

institute: La Jolla Institute for Allergy and Immunology

summary: Follicular regulatory T cells (TFR cells) and their functional role in cancer have been completely disregarded so far. Our data identify that as a critical oversight, as these cells account for a substantial proportion of tumor-infiltrating CD4+ T cells

overall_design: Assessment of the transcriptomic profile of TREG and TFR cells in an immunization setting

first: Simon

last: Eschweiler

first: James

last: Clarke

first: Ciro

last: Ramirez Suastegui

first: Bharat

last: Panwar

first: Ariel

last: Madrigal

first: Serena

middle: J

last: Chee

first: Edwin

last: Woo

first: Aiman

last: Alzetani

first: Peter

last: Friedmann

first: Tilman

last: Sanchez-Elsner

first: Ferhat

last: Ay

first: Christian

last: Ottensmeier


title: Intratumoral TFR cells curtail anti-PD-1 treatment efficacy [human]

overall_design: Assessment of the transcriptomic profile of tumor-infiltrating TREG and TFR cells


title: Small molecule-inducible RNA-targeting systems for temporal control of RNA regulation

status: Public on May 02 2021

city: Chicago

first: Bryan

last: Dickinson

department: Chemistry

institute: The University of Chicago

summary: Programmable RNA-targeting tools provide the unique opportunity to study RNA regulation and control gene expression in an endogenous environment. However, the temporal control over these systems is lacking, rendering studies on the temporal control of regulation challenging. Here, we report the development of a small molecule-controllable RNA effector system to overcome this challenge.

overall_design: RNA-seq experiments were performed on mRNA extracted from HEK-293T cells with one biological replicates; we sequenced two conditions: without small molecule (- ABA) and with small molecule (+ABA)

first: Simone

last: Rauch


title: A novel multidrug-resistant cell line from an Italian intrahepatic cholangiocarcinoma patient

status: Public on May 01 2021

city: Biella

first: Paola

last: Ostano

address: via Malta 3

country: Italy

institute: Fondazione Edo ed Elvo Tempia

summary: Chemotherapy resistance is a relevant clinical issue in the tumor treatment, in particular in biliary  tract carcinoma (BTC), for which there are no effective therapies, neither in the first nor in the  second line. The development of chemoresistant cell lines as experimental models to investigate the  mechanisms of resistance and identify alternative druggable pathways is mandatory. In BTC, in  which genetics and biological behavior depend on the etiology, ethnicity and anatomical site of  origin, the creation of models that better recapitulate these characteristics is even more crucial.  Here we have established and characterized an intrahepatic cholangiocarcinoma (iCCA) cell line  derived from an Italian patient, called 82.3. Cells were isolated from a patient-derived xenograft  and, after establishment, immunophenotypic, biological, genetic, molecular characteristics and  tumorigenicity in vivo in NOD/SCID mice were investigated.  82.3 cells exhibited epithelial morphology and cell markers (EPCAM, CK7 and 19); they also  expressed different cancer stem markers (CD44, CD133, CD49b, CD24, Stro1, PAX6, FOXA2,  OCT3 / 4) and under anchorage-independent and serum-free conditions were capable of originating  cholangiospheres. The population doubling time was approximately 53 hours. In vitro they  demonstrated a poor ability to migrate, but in vivo, 82.3 cells retained their tumorigenicity, with a  long latency period (16 weeks). Genetic identity using DNA fingerprinting analysis revealed 16  different loci and the cell line was characterized by a complex hyperdiploid karyotype.  Furthermore, 82.3 cells showed cross-resistance to gemcitabine, 5-fluorouracil, carboplatin and  oxaliplatin; in fact their genetic profile showed that in a panel of genes (n = 168), specific for drug  resistance and related to the epithelial-mesenchymal transition, 60% of them were deregulated in  82.3 cells compared to a control iCCA cell line sensitive to chemotherapeutics.  In conclusion, we have created new iCCA cell line of Caucasian origin that could be exploited as a  preclinical model to study drug resistance mechanisms and to identify alternative therapies to  improve the prognosis of this tumor type.

overall_design: Transcriptomic analysis of two multidrug resistant cholangiocarcinoma cell lines, 82.3 and MT-CHC01R1.5, compared to the sensible MT-CHC01 cell line

first: Caterina

last: Peraldo-Neia

first: Annamaria

last: Massa

first: Marco

last: Basiricò

first: Chiara

last: Raggi

last: Bernabei

first: Laura

last: Casorzo

first: Mara

last: Panero

first: Francesca

last: Vita

first: Francesco

last: Leone

first: Giuliana

last: Cavalloni

first: Massimo

last: Aglietta


title: Intratumoral TFR cells curtail anti-PD-1 treatment efficacy

first: Pandurangan

last: Vijayanand

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Epigenome analyses implicate ILC2s as key mediators of allergic airway inflammation

city: Rotterdam

first: Ralph

last: Stadhouders

address: Dr. Molewaterplein 50

department: Pulmonary Medicine

country: Netherlands

institute: Erasmus Medical Center

summary: Group 2 innate lymphoid (ILC2) cells are major producers of the cytokines that drive allergic asthma and elevated levels of ILC2s have been detected in the blood and sputum of asthma patients. Asthma susceptibility has strong (epi)genetic components, but the underlying mechanisms and whether they are linked to ILC2 biology remain unclear. To reveal the molecular basis of ILC2 function in allergic airway inflammation (AAI) and assess its relevance for understanding how genetic variation affects asthma susceptibility. Gata3-IRES-YFP reporter mice were used to isolate ILC2s from bronchoalveolar lavage fluid and lymph nodes. Human naive ILC2s were purified from peripheral blood and activated in vitro. We employed RNA-Seq, ChIPm-Seq and computational approaches to study the transcriptome and epigenome in the context of ILC2 activation, tissue-specific functions and genetic susceptibility to asthma. Activated ILC2s displayed a tissue-specific gene expression signature that emerged from a highly similar epigenome. We identify superenhancers - a class of regulatory regions susceptible to epigenetic drugs - controlling ILC2 identity and asthma-associated genes. The majority of genes implicated in asthma by genome-wide association studies resided in an active or primed state in ILC2s. A substantial number of asthma-associated genetic variants were found in ILC2 gene regulatory elements. Our genome-wide analyses reveal new potential functions for ILC2s in AAI, which possess a plastic and flexible epigenome. Importantly, we reveal a strong link between gene regulatory mechanisms in ILC2s and the (epi)genetic basis of asthma susceptibility, supporting a pathogenic role for ILC2s in human asthma.

overall_design: Biological replicate (n=2-4) ChIP-Seq and RNA-Seq

first: Rudi

last: Hendriks


title: Gsx1 Promotes Locomotor Functional Recovery After Spinal Cord Injury

city: Piscataway

first: Li

last: Cai

state: NJ

address: 599 Taylor Road, Rutgers, Rutgers University

department: Biomedical Engineering

institute: Rutgers University

summary: Promoting residential cells, particularly endogenous neural stem and progenitor cells (NSPCs), for tissue regeneration represents a potential strategy for the treatment of spinal cord injury (SCI). However, adult NSPCs differentiate mainly into glial cells and contribute to glial scar formation at the site of injury. Gsx1 is known to regulate the generation of excitatory and inhibitory interneurons during embryonic development of the spinal cord. Here we show that lentivirus-mediated expression of Gsx1 increases the number of NSPCs in a mouse model of lateral hemisection SCI during the acute stage. Subsequently, Gsx1 expression increases the generation of glutamatergic and cholinergic interneurons and decreases the generation of GABAergic interneurons in the chronic stage of SCI. Importantly, Gsx1 reduces reactive astrogliosis and glial scar formation, promotes 5-HT neuronal activity, and improves the locomotor function of the injured mice. Moreover, RNA-seq analysis reveals that Gsx1-induced transcriptome regulation correlates with NSPC signaling, NSPC activation, neuronal differentiation, and inhibition of astrogliosis and scar formation. Collectively, our study provides molecular insights for Gsx1-mediated functional recovery and identifies Gsx1 gene regulation as a potential application for injuries in the spinal cord and possibly other parts of the central nervous system.

overall_design: Spinal cord tissues of 3, 14, 35 days post-injury (DPI) were isolated and segments containing injured/injected (parenchymal segments spanning ~2-3 mm from each side of the lesion) were rapidly snap-frozen in liquid nitrogen. Total RNA was isolated from spinal cord tissues using the RNeasy Lipid Tissue Mini kit (Qiagen, #74804) following the manufacturer’s protocol. The concentration of the total RNA was determined using Qubit RNA BR Assay Kit (Life Technologies) and quality of the total RNA was determined using the RNA 6000 Nano chip on the 2100 Bioanalyzer automated electrophoresis system (Agilent Technologies).

first: Misaal

last: Patel


title: ppGpp signal plays critical role in pathogenesis of Acinetobacter baumannii 17978

city: Daegu

first: Md.

middle: Maidul

last: Islam

address: 680 Gukchaebosang-Ro, Jung-gu

department: Department of Microbiology

institute: Kyungpook National University

summary: Acinetobacter baumannii is a major cause of nosocomial infections which can survive in different hospital environments and its multidrug-resistant capacity is major concern now-a-days. ppGpp dependent stringent response mediates reprogramming of gene expression with diverse function in many bacteria. A baumannii A1S_0579 gene is responsible for ppGpp production. Transcriptome analysis of early stationary phase cultures represents several differentially expressed genes in ppGpp deficient strain (∆A1S_0579). We found that the expression of csu operon, which is important in pili biosynthesis for early biofilm formation, was significantly reduced in the ppGpp-deficient strain. Our findings showed that ppGpp signaling plays critical role in biofilm formation, surface motility, adherence and virulence of A baumannii. This study is the first demonstration of the association between ppGpp and pathogenicity of A. baumannii.

overall_design: RNA-seq of total RNA extractions from A. baumannii 17978 wild-type, ∆A1S_0579 mutants grown at 37 ºc upto early stationary phage

first: Kyeongmin

last: Kim

first: Md

first: Minsang

last: Shin